Biology subjects

Gribskov, M.

Publications and source records attributed to Gribskov, M..

6 recordsLinked to original sources

bioRxiv2026

Sorghum ANTHRACNOSE RESISTANCE GENE3 Is a Non-Coding RNA That Confers Fungal Resistance through Enhanced Cell Death

The fungal pathogen Colletotrichum sublineola is a major constraint to sorghum production. The sorghum genotype IS18760 is resistant to multiple C. sublineola strains, but the genetic basis of this resistance is unknown. Bulk segregant analysis using whole-genome resequencing of a biparental mapping population identified a major resistance locus, designated ANTHRACNOSE RESISTANCE GENE LOCUS 3 (ARG3), associated with extensive cell death. Fine mapping delimited the ARG3 locus to a 30 kb interval containing three predicted protein-coding genes and one unannotated non-coding RNA gene. Among these, only the non-coding RNA gene showed consistent sequence polymorphisms between resistant and susceptible lines and elevated pathogen-induced expression in the resistant parent, suggesting that it underlies ARG3-mediated resistance. Regions syntenic to ARG3 across grass species contain conserved non-coding sequences enriched for H3K27me3 and H2A.Z chromatin marks, suggesting a conserved regulatory function. The resistance allele is absent from a 111-line sorghum pangenome. The resistant sorghum line harboring ARG3 and the corresponding avirulent pathogen strain originate from the same geographic region, suggesting co-evolution between host resistance and a prevalent pathogen strain. Phylogenetic analysis suggests that loss of resistance in susceptible lines may relate to insertion of a 12.4 kb repetitive sequence. Importantly, silencing of the ARG3 transcript in the resistant parental line abrogated resistance to C. sublineola, confirming that ARG3 non-coding RNA gene underlies the fungal resistance mediated by the ARG3 locus in IS18760. These lines of evidence show that ARG3 is an important target for resistance breeding and provide new insight into non-coding RNA-mediated disease resistance.

plant biology↗

bioRxiv2025

Functional Characterization of Zymoseptoria tritici Candidate Effectors Reveals Their Role in Modulating Immunity in Nicotiana benthamiana

Zymoseptoria tritici is a significant wheat pathogen responsible for Septoria tritici blotch (STB) disease. Despite its economic impact, understanding of the molecular interactions between Z. tritici and its host remains limited, particularly the functions of many uncharacterized candidate effectors. Here, we assessed seven Z. tritici candidate effectors with elevated expression during the early biotrophic phase and transition to necrotrophy by transiently expressing them in the heterologous, non-host system Nicotiana benthamiana, with and without their predicted signal peptides. AlphaFold structural predictions revealed that two candidates share similarity with proteins of known function: a sterol-binding protein from Saccharomyces cerevisiae and a necrosis-inducing effector from the apple canker pathogen Valsa mali. Effector-associated phenotypes did not always correlate with expression timing, and signal peptide presence significantly influenced observed activities. Because N. benthamiana is not a natural host of Z. tritici, observed responses may reflect conserved, host-independent activities of effectors or immune recognition by N. benthamiana, rather than their native functions in wheat. Consistent with this distinction, two candidate effectors, Mycgr3107904 and Mycgr394290, induced cell death in N. benthamiana while also modulating ROS burst, likely indicative of immune recognition. Some candidates attenuate ROS production, suggesting potential targeting of conserved cellular processes, whereas none suppress PBR1-mediated cell death. Overall, our results indicate that candidate effector activities cannot be inferred from expression profiles alone, and that responses in the non-host N. benthamiana system reflect a combination of immune recognition and potential conserved activities, and primarily serve to prioritize candidates for validation in the native wheat-Z. tritici interaction.

molecular biology↗

bioRxiv2025

Differences Among Fungal Microbiomes Associated with Tar Spot of Corn in Ecuador, Guatemala, and Indiana, USA

Tar spot of corn, caused by the obligate fungal pathogen Phyllachora maydis, was previously found to be associated with Monographella maydis (syn. Microdochium maydis) and Coniothyrium phyllachorae in Mexico. While M. maydis was once believed to cause fisheye lesions and C. phyllachorae was described as a mycoparasite of P. maydis, their presence and roles in tar spot remain uncertain. This study hypothesizes that the tar spot-associated fungal microbiome varies geographically and includes fungal species with inconsistent associations with the disease. To test this, tar spot-infected leaves were collected in Guatemala, Ecuador, and the USA. This study shows that the distribution and abundance of these fungi exhibit a geographical pattern and are not consistently associated with tar spot lesions in all locations. We confirmed the presence of Microdochium in some parts of Ecuador and Guatemala but not in the USA. The role of Microdochium remains unclear and whether it can be a primary pathogen needs to be tested by additional research, as its occurrence and abundance depend more on geographical locations rather than the presence of fisheye lesions. Coniothyrium was detected at low abundance in samples from Ecuador and Guatemala but was absent in the USA. Additionally, we identified the likely mycoparasite Paraphaeosphaeria as highly prevalent across samples from all three countries. Microbiome diversity analysis grouped tar spot samples into four distinct clusters: two dominated by P. maydis, one primarily associated with Microdochium, and a fourth characterized by a combination of P. maydis and Paraphaeosphaeria.

plant biology↗

bioRxiv2023

Mechanisms of infection and response of the fungal wheat pathogen Zymoseptoria tritici during compatible, incompatible and non-host interactions

Zymoseptoria tritici is responsible for Septoria tritici blotch, a disease causing significant annual yield losses in wheat. To investigate infection phase-specific gene expression in the pathogen, we analyzed gene expression during infection of susceptible (Taichung 29) and resistant (Veranopolis and Israel 493) wheat cultivars, plus the non-host species barley at 1, 3, 6, 10, 17 and 23 days post inoculation (DPI). There were dramatic differences in pathogen gene expression at 10 DPI in the susceptible compared to both resistant interactions. The most pronounced differences in pathogen gene expression were observed at 3 DPI in both the susceptible and resistant host interactions compared to the non-host interaction. Thirty-one putative effectors showed early expression during the susceptible interaction compared to the non-host interaction, and six effectors were selected for subcellular localization studies. Using Agrobacterium-mediated transient expression in Nicotiana benthamiana, subcellular localization assays revealed that two candidate effectors, Mycgr3109710 and Mycgr394290, localized to putative mobile cytosolic bodies when expressed without their signal peptides, suggesting potential roles in intracellular signaling or host gene regulation. When expressed with their native signal peptides, four candidate effectors localized to the cytosol, while one effector, Mycgr3107904, did not accumulate to detectable levels, as shown by immunoblot analysis, indicating degradation. Comparison of pathogen gene expression in the susceptible host to expression in the resistant hosts, allowed us to identify genes that are expressed during the transition from biotrophic to necrotrophic growth at 10 DPI. Comparison of pathogen gene expression in resistant and susceptible hosts, versus in the non-host barley, allowed us to identify genes involved in initial colonization and host recognition. In addition, our study contributes to understanding candidate effectors that are activated early during infection and may play a role in the initial suppression of plant immunity, making them strong candidates for functional characterization.

plant biology↗

bioRxiv2019

The evaluation of RNA-Seq de novo assembly by PacBio long read sequencing

RNA-Seq de novo assembly is an important method to generate transcriptomes for non-model organisms before any downstream analysis. Given many great de novo assembly methods developed by now, one critical issue is that there is no consensus on the evaluation of de novo assembly methods yet. Therefore, to set up a benchmark for evaluating the quality of de novo assemblies is very critical. Addressing this challenge will help us deepen the insights on the properties of different de novo assemblers and their evaluation methods, and provide hints on choosing the best assembly sets as transcriptomes of non-model organisms for the further functional analysis. In this article, we generate a \"real time\" transcriptome using PacBio long reads as a benchmark for evaluating five de novo assemblers and two model-based de novo assembly evaluation methods. By comparing the de novo assmblies generated by RNA-Seq short reads with the \"real time\" transcriptome from the same biological sample, we find that Trinity is best at the completeness by generating more assemblies than the alternative assemblers, but less continuous and having more misassemblies; Oases is best at the continuity and specificity, but less complete; The performance of SOAPdenovo-Trans, Trans-AByss and IDBA-Tran are in between of five assemblers. For evaluation methods, DETONATE leverages multiple aspects of the assembly set and ranks the assembly set with an average performance as the best, meanwhile the contig score can serve as a good metric to select assemblies with high completeness, specificity, continuity but not sensitive to misassemblies; TransRate contig score is useful for removing misassemblies, yet often the assemblies in the optimal set is too few to be used as a transcriptome.

bioinformatics↗

bioRxiv2019

Chromatin-enriched RNAs mark active and repressive cis-regulation: an analysis of nuclear RNA-seq

Long noncoding RNAs (lncRNAs) localize in the cell nucleus and influence gene expression through a variety of molecular mechanisms. RNA sequencing of two biochemical fractions of nuclei reveals a unique class of lncRNAs, termed chromatin-enriched nuclear RNAs (cheRNAs) that are tightly bound to chromatin and putatively function to cis-activate gene expression. Until now, a rigorous analytic pipeline for nuclear RNA-seq has been lacking. In this study, we survey four computational strategies for nuclear RNA-seq data analysis and show that a new pipeline, Tuxedo, outperforms other approaches. Tuxedo not only assembles a more complete transcriptome, but also identifies cheRNA with higher accuracy. We have used Tuxedo to analyze gold-standard K562 cell datasets and further characterize the genomic features of intergenic cheRNA (icheRNA) and their similarity to those of enhancer RNA (eRNA). Moreover, we quantify the transcriptional correlation of icheRNA and adjacent genes, and suggest that icheRNA may be the cis-acting transcriptional regulator that is more positively associated with neighboring gene expression than eRNA predicted by state-of-art method or CAGE signal. We also explore two novel genomic associations, suggesting cheRNA may have diverse functions. A possible new role of H3K9me3 modification coincident with icheRNA may be associated with active enhancer derived from ancient mobile elements, while a potential cis-repressive function of antisense cheRNA (as-cheRNA) is likely to be involved in transiently modulating cell type-specific cis-regulation.\n\nAuthor SummaryChromatin-enriched nuclear RNA (cheRNA) is a class of gene regulatory non-coding RNAs. CheRNA provides a powerful way to profile the nuclear transcriptional landscape, especially to profile the noncoding transcriptome. The computational framework presented here provides a reliable approach to identifying cheRNA, and for studying cell-type specific gene regulation. We found that intergenic cheRNA, including intergenic cheRNA with high levels of H3K9me3 (a mark associated with closed/repressed chromatin), may act as a transcriptional activator. In contrast, antisense cheRNA, which originates from the complementary strand of the protein-coding gene, may interact with diverse chromatin modulators to repress local transcription. With our new pipeline, one future challenge will be refining the functional mechanisms of these noncoding RNA classes through exploring their regulatory roles, which are involved in diverse molecular and cellular processes in human and other organisms.

genomics↗